Another chance to be your man
by Jojo1112
Summary: When Reese rescued Root at the beginning of Season 5, he could not have known what kind of conflict and mental turmoil he set in motion while saving the Machine and lives together again. Rare pairing (Reese/Root)!


**A/N**

This is a follow-up to 'New Chances'. Remember: **this a rare pairing story** (Reese/Root).

Thank you:

 _ClaudiaRain_ for help, encouragement, continuation and second eyes

 _Lizzy_ for inspiration and being a real lovely friend

 _jteam6920_ (for having an idea in common ;-) and PlumeViolette and afreshwatermaid (haven't heard from you in a while?!)

 _Windcage_ (although from a different fandom!) for always coming up with new ideas

 _EX eccentric_ for being such a positive inspiration (check the wonderful youtube video of Root and Reese!)

Whenever I refer to the Machine as _she_ or _her_ it is printed in italics.

Quotes at the beginning are mostly taken from scenes with Reese and Root in Season 5.

* * *

" **Always knew you had a soft spot for me."**

" **There's no god mode anymore. The Machine's down... Finch needs you back at the subway. Higher calling."**

" **And leave you here?** "

(S05E01)

Those words. Today. Root had said them easily, almost mockingly, he was certain, but they started to haunt him. He had thought he'd found some peace in between the chaos of his feelings, but it didn't seem so. Wasn't it time to be honest?

Iris was lovely, was patient, knew and read him well, but then again, he put her constantly in danger simply by spending time with her. Never mind the added stress of his side job (in truth his real job, not the police work he was forced to do now over a year) and the possibility of his cover being blown every moment.

His thoughts drifted to another time.

* * *

 _Approximately fifteen months earlier... (between S03/S04)_

 _One day, Root wasn't there in the morning to pick him up from work (as a security guard for a big tech company). John went home to his apartment, looking for her there. No note on the kitchen table._

 _Maybe she had a bigger errand to run, he thought. Or had to change cover again. A slight uncertain feeling accompanied him, but he was so tired that he climbed onto his bed and slept within seconds._

 _When he woke up – around noon, he guessed – it was because of her arms around him, her head against his back._

 _He wasn't sure, but he heard her... crying?_

" _Wildcard?" He only whispered, questioning, instinctively knowing the way she held him tight she needed some minutes to stay there._

" _Talk to me."_

 _It took an amount of time before she calmed down and all he could do was to stroke her hands. Waiting for her to explain._

" _Tomorrow, you have a new job." She said, low. Exasperated._

" _What happened?" He rasped, after a while._

" _Samaritan... kind of rebooted parts of itself. Our handcrafted servers had to choose... new cover identities..." She whispered. "There's nothing her and I... could have done to prevent it..."_

 _John immediately knew what was coming._

" _We have to move?" He said. It wasn't said easily, but with a slight acceptance of the inevitable he had feared would come sooner or later._

" _John..."_

 _Desperation took her over and he could feel her silent struggle again. Finally, the tension and the pressure of her arms stopped so he could turn around and watch her, fighting with tears._

" _It's alright." He tried to soothe her. Calm her. What else could he do?_

" _No, it's not." She said, defiantly. Broke free from his hold._

" _It means we all... have to start from the beginning. You and me, too."_

" _It doesn't matter..." John didn't get far._

" _It matters to me, John. I don't want to... give you up. I don't want you to... leave. I don't want us to... stop this..."_

 _John had rarely heard Root speaking that passionately of him._

" _We can begin again." He said to her, grabbing for her, but she moved back._

" _Too dangerous."_

" _If this is our last day in these covers, stay with me for this day, wildcard."_

" _You just break my heart, John."_

* * *

Those words. The look she gave him when she had recognized it was _him_ who came to her rescue. A look he would probably never forget and he was cursing himself that he couldn't get her out of his head _again_.

But he simply couldn't stop thinking of her.

Nothing had prepared him for the full impact of Samaritan being in charge. His former job – working for the CIA, before he had met Harold – had taught him a lot of things. Quickly slipping into different personas had been one part of it, but his new and latest cover, working as Detective John Riley for over a year now, took way too long for his taste. Although they had been getting social security numbers, lives to safe, he always found himself handicapped by his day job.

Including the persuasive work to bring Harold back in the game. Fortunately, Shaw had been only too happy to come along again. And Root, of course.

But her looks had been in Shaw's direction since they parted and John couldn't tell if it was on purpose, to signal to him there was no room for him anymore. As he had always suspected she had a crush on Shaw, he wasn't jealous, not of Shaw who had been more pissed most of the time than turned on, but he was... somehow hurt. He had let Root in, fought against it (and then for it so long), and when it finally happened... he was forced to let her go.

When he told Iris of his habit to protect, he had not only meant Jessica and Joss, a little part was dedicated to Root, too.

Why did he still think about it so much? It was another part... he would carry with him until the end. And it seemed the end was far nearer than anybody had ever expected before.

He sighed. Nothing else he could do other than trying to push his desperation and his real feelings to the back of his mind to be able to sleep, when another memory crawled in.

* * *

 _Some months earlier, Election Day (around S04E05 "Prophets")_

 _After this exhausting night (and day, only spent at the damn police desk, since he was on desk duty) it had felt good to save this young talented man, a gifted political pollster. When John finally came home, knowing another day would follow at the precinct, stuck at this desk to survive, which frustrated him more than anything, he had fallen into his bed and almost slept – but suddenly he heard his door open. He stood immediately on alert, and it nearly threw him when Root showed up in the doorstep of his bedroom, completely disheveled and obviously wounded._

 _She smiled in a way only she could smile at him. "I'm sorry to disturb your beauty sleep."_

 _Then she sighed, almost dramatically. "We really need your help."_

 _There was a sudden tension in the room that wasn't there before._

 _He gripped her tightly, not knowing if he should laugh or be angry about the situation. Her timing was always impeccable._

" _What are you really doing here?" He asked Root as calmly as he could._

" _Checking on you? - I need your first-aid kit."_

 _The tone went from mocking to serious and Root opened her jacket, let John see the bullet that was still in her shoulder and the profound bleeding._

" _You..."_

 _In one fluid moment, John had shoved her into his bathroom and directed her onto the WC and grabbed for his bandages and disinfectant._

" _You still have that whiskey of yours?" Root asked him in between. "I could use a drink..."_

 _John had inspected her wound and seen that he needed more time to stitch it._

" _I'll go get the whiskey." He said to her and stood. "You wait here, okay?"_

 _Root smiled to him very sweetly. "Yes, Sir."_

 _He rolled his eyes and was already outside. Root really only brought him difficulties..._

 _He took the bottle of whiskey and returned into his bathroom, where Root was almost sprawled on his WC. Sleeping? Or passed out?_

 _The latter would make things much easier for him._

 _But when he touched her shoulder, softly, probing to find the bullet, her big eyes were back on him. "No need to fuss over it." Was all she snapped, quoting his words from a while ago._

 _He sighed. "Will you just be quiet and let me help you?" He put the whiskey bottle in her hands. And started working on the wound, careful, patient._

 _She hissed and gulped her first big swig when he pulled the scalpel and got the bullet out. A stream of blood came with it, and Root almost in his hands, at the edge of losing consciousness._

" _Hold still." He said to her, leaned her against the toilet tank and tried to disinfect and bandage the big wound to stop the bleeding._

" _Easier said than done." Was her comment. Then. "I knew you kinder, John. That police job really got you, ha?"_

 _Another big shot of the whiskey._

 _Since she wavered slightly from one side to the other, he just held her tighter. "Stop, otherwise I..."_

" _I can do it myself, John." She said to him impatiently, freed herself from his hold, grabbed a bandage – and lost her balance, landing on the floor._

" _No need to fall at my feet for that." He replied dryly and picked her up. She fought against him._

" _Just let me go!"_

 _She wanted to play the resistant one? Then why did she come here? Sometimes he was simply fed up with her... but when she started to fall again, he just took her in his arms and went back into his bedroom. Laid her down on his bed. She had begun to fight him again, but when he put her down, she stopped. A gasp. And a sudden jolt made her vomit the whiskey beside his bed._

 _This was just great._

 _Root fell back, pale, silent. Her wound had started bleeding again._

" _Damn it, Root." He said to her. Angry. "Stay here. Don't move. I'll be back."_

 _He went back to the bathroom, went for the second time for his first aid kit and took his cleaning things along and returned._

 _First, he cleaned the floor and opened a window for fresh air. Root had passed out due to the pain. When he saw her curled up on his bed – as she so often had done when they had been together - , his anger diminished. She really looked very exhausted. And somehow, he missed the time when it had just been the two of them._

 _Cautiously, he undressed her – was reminded again of so many passionate moments, still knowing every inch of her body – and took care of her wound again and put her finally under his sheets._

 _To distract him from his thoughts, he cleaned his kitchen. Shot a look from time to time into his bedroom to see if she was okay and finally came back when housework was done._

 _First, he sat on the stool on the other side of his bed, where he normally put his clothes, and took the liberty of simply watching her, mulling over what to do. What had made her come to him? But he was very tired and knew that a lot waited for him at the precinct tomorrow, so he stopped his thoughts, stepped out of his clothes and slid beside her. They had spent so many nights together, it was a natural thing to do. Since she was cold, he pulled her close to him, her back to his chest, wrapping himself around her, warming her and simply holding her._

 _He realized again how much he had missed that, just holding her, fitting so perfectly in his arms, feeling so good there. John closed his eyes. How much he missed all... of her. Even her mocking, which he had come to accept as a part of her._

 _But this was all he would ever get. As close as he would ever get again. Spooning her... was too good to be true, and slowly he realized how his body reacted to her nearness. He couldn't do anything against it although he tried. There was some part in him that still had all the feelings for Root preserved - and didn't want them to give up._

" _Sorry." He breathed in her ear and he put all his feelings into it. Started to relax himself in spooning her and slept, at last._

 _Root woke up in a warm embrace she knew very well. Feeling protected. Nobody made her feel that way except him, not even Shaw, who was busy with Romeo and his gang of thieves, anyway. It was a need only John understood and was able to give to her. Damn. A part in her wanted to jump out of his bed at once and run away. The other part wanted to stay so badly that she gave in. She heard that he slept so she made no big moves that could wake him up, just huddled a bit closer against him. Wanted to feel safe for a moment, again. The sudden hurt in her shoulder – that was freshly bandaged, she could see, had he done that while she was out? - made her realize that her heart hurt, too. Root missed John... more than he knew. All her tough phrases were a shield to protect her from the feelings for him that were still there. She had thought it would all go away once she won Shaw, but John was secretly with her wherever she went. His care... that he had won her heart with, and his love... so surprising and tender, unlike anyone she had ever met before. That's why he was the first on her mind to run to when she had finally managed to escape the shootout and the wild chase with Martine. And that talk with Harold that had shaken her to the core because he had keenly observed that she was living without the Machine now. A talk about caring and being scared had followed which had left her uneasy as well – and the word 'caring' was always connected to John..._

 _Harold had seen how lonely she felt, how lost she seemed, and wasn't he right? Loosing the connection to the Machine, because if she talked Samaritan would see, had hurt her a lot. But she had to keep going. And she should really stop her rattling train of thoughts._

 _Suddenly, she could hear his whisper in her ear: "Stop thinking and go back to sleep, wildcard. You need it."_

 _She squeezed his hand that rested on her belly, still warming her although her body temperature was better now, realizing how unfair it was that they had needed that first break because of Samaritan to find each other, and were forced to part by the second break. He still called her 'wildcard', his personal term of endearment for her?_

" _John." Root murmured. "Stop being so nice to me."_

 _He paused one moment and whispered again: "Tried. Can't. Don't know why. - How's your shoulder?"_

" _Better." She whispered back, not knowing what else to say._

" _Then sleep. You'll need it."_

 _Root hesitated one moment, but couldn't resist trying. "John?"_

 _Again his warm, raspy voice. "What else?"_

" _Can I... stay this night?" She queried low._

 _His answer in her ear was telling. "You are always welcome here."_

" _Am I?"_

 _He sighed. "I didn't change the rules."_

 _Root squeezed his hand again. "Sorry."_

" _I'm not sorry that you're here right now. So don't be." He answered. "Now go back to sleep."_

 _She wanted to. Sleep meant forgiveness and forgetting. But she couldn't. He was so close, would she ever get a chance to be this close to him again?_

 _At a loss for words, she led his hand to the sensitive and hot spot between her legs. His head sank against her back and she could feel his silken hardness nudging against her ass._

" _Don't... do that to me, wildcard." He breathed. Groaned, when she did circles with his fingers. "I can't..."_

" _Me neither." She whispered._

 _John was getting high on her, he couldn't deny it. For the moment, he couldn't have resisted her even if he tried. Passion. Ecstasy. Sensational feelings... it was all still there. But it was not the right moment._

" _Wait." He rasped again._

 _Root stopped. "Alright. Your way."_

 _He couldn't stop himself from smiling although the situation was far from perfect. "I missed you saying that to me..."_

 _She laughed out loud by the happy memories that rained down on her, couldn't suppress it. And in that same moment, pain went through her. Root gasped._

 _He stopped for a moment, touched softly at her bandages, but everything seemed okay. Still holding her tight._

" _Don't stop." Root whispered. "I... need this... need you to make me high... like the way only you can."_

 _There. She had tried to put some of her feelings in her answer._

" _I'm sorry I can't..." John said with a lot desperation. "Not in a situation like this."_

 _She sensed his hesitations for some seconds. And although she stretched her wounded shoulder, she turned to him because she wanted to look him in the eyes._

" _But you're important to me."_

 _John remained quiet for a moment. This was getting out of hand._

" _Wildcard." He said softly, then. "Sleep. Please."_

 _But her look went down to his still hard-on, and she knew. But when she touched his silken shaft, John took her hand away._

" _No." Was all he said._

 _Root watched him, tears welling up in her eyes, but John simply couldn't bring himself to say any other words... as confused and tired that he was, there was something in him that couldn't give entirely in to her, suspecting that she had only sought shelter for one night and nothing else._

" _I understand. Thank you." Was all she answered in an automatic way._

 _In one moment she went up, gathered her clothes and left his apartment._

 _Leaving John behind, cursing himself and his stubbornness. He wanted to turn the time back... wanted to have her back. Completely, without compromise. He fell back into the sheets that still smelled of her. The longing consumed him again. Damn._

* * *

Those words. They haunted him in his sleep. Where had the 'soft spot for her' taken him?

The next morning brought nothing more than work again, although it felt better now, more easily done and Lionel not an adversary, but a partner. Because he knew Harold and Root were working on the awakening of the Machine, he had installed some cameras into the precinct and tried to get them to work with their help. He still couldn't believe they had gathered 'play stations' to save the Machine, but it was as it was...

And the subway quarters were safe for now. Safe, until the next thing came along. Root now chose to live with Harold down there, and she seemed to be quite content about it. This arrangement made it possible for him to see her every day from now on – but did he really want that?

At least Harold was there, and the best thing to protect John from a rushed reaction _because_ he still had no explanation for these feelings, for what had happened between them, and why they were so lively in his mind again.

Whatever this was... one part of him fanatically wished for it back, although knowing full well he shouldn't for his own sake.

Wasn't it time to make a decision?


End file.
